Principles of Biology: Study Guide for Unit 1 – Biological Molecules, Chemistry, and Membranes

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Biology: The Study of Life

Proximate and Ultimate Explanations

Biological phenomena can be explained at different levels. Proximate explanations address the immediate mechanisms underlying a process, while ultimate explanations focus on the evolutionary reasons for why a process occurs.

Proximate Explanation: Explains how something happens (mechanism, physiology, development).
Ultimate Explanation: Explains why something happens (evolutionary history, adaptive significance).
Example: Birds migrate (proximate: hormonal changes in response to day length; ultimate: migration increases survival and reproductive success).

Experimental Design in Biology

Sound experimental design is essential for testing hypotheses and drawing valid conclusions.

Key Features: Control groups, replication, randomization, and minimizing confounding variables.
Hypotheses: Must be testable and falsifiable.
Predictions: Specific outcomes expected if the hypothesis is correct.
Evaluating Experiments: Assess if controls are present, variables are isolated, and sample size is adequate.

Chemistry: The Chemical Basis of Life

Atomic Structure and Chemical Bonds

Atoms are the fundamental units of matter, composed of protons, neutrons, and electrons.

Atomic Structure: Protons (+), neutrons (0), electrons (−) arranged in shells.
Element Differences: Determined by atomic number (number of protons).
Bond Types:
- Covalent Bonds: Atoms share electrons (e.g., H2O).
- Ionic Bonds: Electrons are transferred, creating charged ions (e.g., NaCl).
- Hydrogen Bonds: Weak attractions between polar molecules (e.g., between water molecules).
Properties: Bond type affects molecule stability, melting/boiling points, and solubility.

Water: Structure and Properties

Water's unique properties arise from its polar covalent bonds and ability to form hydrogen bonds.

Structure: Two hydrogen atoms covalently bonded to one oxygen atom.
Bonding: Covalent bonds within a molecule; hydrogen bonds between molecules.
Partial Charges: Oxygen is partially negative (δ−), hydrogens are partially positive (δ+).
Properties: High specific heat, high heat of vaporization, cohesion, adhesion, solvent abilities.
Biological Importance: Moderates temperature (e.g., sweating, coastal climates).

Acids, Bases, and pH

The pH scale measures hydrogen ion concentration in a solution.

Acid: Substance that increases H+ concentration (pH < 7).
Base: Substance that decreases H+ concentration (pH > 7).
pH Formula:

Relationship: As [H+] increases, pH decreases.
Calculations: A change of 1 pH unit = 10-fold change in [H+].

Carbon-Based Molecules and Energy

Functional Groups

Functional groups are specific groups of atoms within molecules that confer characteristic chemical properties.

Amino (–NH2): Acts as a base.
Carbonyl (–C=O): Found in aldehydes and ketones.
Carboxyl (–COOH): Acts as an acid.
Hydroxyl (–OH): Polar, forms hydrogen bonds.
Methyl (–CH3): Nonpolar.
Phosphate (–PO4): Contributes negative charge, energy transfer.
Sulfhydryl (–SH): Forms disulfide bonds in proteins.

Energy and Thermodynamics in Biology

Energy transformations are central to life. The laws of thermodynamics govern these processes.

First Law: Energy cannot be created or destroyed, only transformed.
Second Law: Entropy (disorder) of the universe tends to increase.
Gibbs Free Energy (): Determines if a reaction is spontaneous.

Endergonic: (requires energy input).
Exergonic: (releases energy, spontaneous).
Reaction Coupling: Exergonic reactions can drive endergonic reactions.

Enzymes and Reaction Graphs

Activation Energy: Energy required to start a reaction.
Enzymes: Lower activation energy, increase reaction rate, do not change .

Graph Interpretation: Enzyme lowers the peak (activation energy) but reactants and products remain the same.

Biological Molecules

Macromolecules: Proteins, Nucleic Acids, Carbohydrates, Lipids

Biological macromolecules are polymers built from monomers (except lipids).

Macromolecule	Monomer	Bond	Function
Protein	Amino acid	Peptide bond	Catalysis, structure, transport
Nucleic Acid	Nucleotide	Phosphodiester bond	Information storage, transfer
Carbohydrate	Monosaccharide	Glycosidic linkage	Energy, structure
Lipid	Fatty acid (not true polymer)	Varies (ester bond in fats)	Membranes, energy storage

Protein Structure and Function

Primary Structure: Sequence of amino acids (peptide bonds).
Secondary Structure: Alpha helices and beta sheets (hydrogen bonds).
Tertiary Structure: 3D folding (hydrogen, ionic, disulfide bonds, hydrophobic interactions).
Quaternary Structure: Multiple polypeptides (subunits) assemble.
Function: Enzymes, structural proteins, signaling, transport.
Active Site: Region where substrate binds and reaction occurs.
Enzyme Specificity: Determined by shape and chemical environment of active site.

Nucleic Acids: DNA and RNA

Nucleotide Structure: Sugar (ribose or deoxyribose), phosphate group, nitrogenous base.
DNA: Double helix, antiparallel strands, stores genetic information.
RNA: Single-stranded, various types (mRNA, tRNA, rRNA), involved in protein synthesis and regulation.
RNA World Hypothesis: RNA may have been the first self-replicating molecule.

Carbohydrates

Monosaccharides: Simple sugars (e.g., glucose).
Disaccharides: Two monosaccharides (e.g., sucrose).
Polysaccharides: Many monosaccharides (e.g., starch, cellulose, glycogen).
Structural Polysaccharides: Cellulose (plants), chitin (fungi, arthropods).
Storage Polysaccharides: Starch (plants), glycogen (animals).
Digestibility: Depends on enzyme presence (e.g., humans lack cellulase).
Energy Storage: Polysaccharides are less osmotically active than monomers.

Lipids

Definition: Hydrophobic molecules, not true polymers.
Categories: Fats (triglycerides), phospholipids, steroids.
Fats: Glycerol + 3 fatty acids (energy storage).
Phospholipids: Glycerol + 2 fatty acids + phosphate (membranes).
Steroids: Four fused rings (e.g., cholesterol, hormones).
Saturated vs. Unsaturated: Saturated (no double bonds, solid), unsaturated (double bonds, liquid).
Cis vs. Trans: Cis (natural, bent), trans (artificial, straight).

Membranes and Membrane Transport

Phospholipid Bilayer and Membrane Structure

Bilayer Formation: Phospholipids spontaneously form bilayers in water due to hydrophobic effect.
Membrane Components: Integral proteins, peripheral proteins, carbohydrates, cholesterol.
Fluid Mosaic Model: Membrane is dynamic, with proteins and lipids moving laterally.

Membrane Fluidity and Permeability

Fatty Acid Composition: Unsaturated fatty acids increase fluidity; saturated decrease it.
Cholesterol: Modulates fluidity and stability.
Permeability: Small, nonpolar molecules pass easily; large or charged molecules do not.

Transport Across Membranes

Diffusion: Movement of molecules from high to low concentration.
Osmosis: Diffusion of water across a semipermeable membrane.
Facilitated Diffusion: Passive transport via proteins (channels, carriers).
Passive Transport: No energy required (diffusion, osmosis, facilitated diffusion).
Active Transport: Requires energy (ATP), moves substances against gradient (pumps, co-transporters).
Examples: Sodium-potassium pump, glucose transporters.

Summary Table: Membrane Transport Mechanisms

Mechanism	Energy Required?	Direction	Example
Simple Diffusion	No	High to Low	O2, CO2
Osmosis	No	High to Low (water)	Water movement
Facilitated Diffusion	No	High to Low	Glucose transporter
Active Transport	Yes (ATP)	Low to High	Na+/K+ pump

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